Starting phenix.real_space_refine on Sat Sep 28 05:39:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/09_2024/7u5u_26359.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10000 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 6411 2.51 5 N 1697 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10035 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4983 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 25, 'TRANS': 612} Chain breaks: 3 Chain: "B" Number of atoms: 5052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5052 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 25, 'TRANS': 619} Chain breaks: 3 Time building chain proxies: 7.06, per 1000 atoms: 0.70 Number of scatterers: 10035 At special positions: 0 Unit cell: (88.7145, 128.699, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1900 8.00 N 1697 7.00 C 6411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 11 sheets defined 41.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.853A pdb=" N ILE A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 948 through 952 removed outlier: 3.961A pdb=" N GLY A 952 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 966 removed outlier: 3.613A pdb=" N GLN A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1022 through 1033 removed outlier: 3.617A pdb=" N LEU A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.561A pdb=" N THR A1041 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.514A pdb=" N ALA A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.604A pdb=" N GLY A1120 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1141 removed outlier: 3.593A pdb=" N LEU A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1184 through 1197 removed outlier: 4.042A pdb=" N LYS A1188 " --> pdb=" O ASN A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 removed outlier: 3.914A pdb=" N LEU A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1244 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 3.522A pdb=" N ASN A1269 " --> pdb=" O ILE A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 removed outlier: 3.727A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1340 through 1343 removed outlier: 3.544A pdb=" N LYS A1343 " --> pdb=" O MET A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1343' Processing helix chain 'A' and resid 1344 through 1349 removed outlier: 3.610A pdb=" N MET A1347 " --> pdb=" O LEU A1344 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A1348 " --> pdb=" O ASP A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1361 Processing helix chain 'A' and resid 1379 through 1389 removed outlier: 3.817A pdb=" N PHE A1387 " --> pdb=" O ILE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1418 removed outlier: 3.552A pdb=" N GLN A1418 " --> pdb=" O TYR A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1440 removed outlier: 3.758A pdb=" N LYS A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 removed outlier: 3.929A pdb=" N LYS A1458 " --> pdb=" O GLN A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1485 removed outlier: 3.894A pdb=" N LYS A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A1485 " --> pdb=" O LYS A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1519 Processing helix chain 'A' and resid 1528 through 1545 removed outlier: 3.717A pdb=" N ARG A1538 " --> pdb=" O ASN A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1555 Processing helix chain 'B' and resid 874 through 880 Processing helix chain 'B' and resid 919 through 924 removed outlier: 4.585A pdb=" N GLU B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 919 through 924' Processing helix chain 'B' and resid 943 through 956 removed outlier: 4.162A pdb=" N ARG B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.704A pdb=" N GLU B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B1000 " --> pdb=" O LYS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 removed outlier: 3.826A pdb=" N ARG B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.502A pdb=" N LEU B1030 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1065 Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1084 through 1091 removed outlier: 3.857A pdb=" N ALA B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1107 through 1111 removed outlier: 3.734A pdb=" N GLY B1111 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1132 removed outlier: 3.537A pdb=" N ARG B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 removed outlier: 4.097A pdb=" N GLU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1188 Processing helix chain 'B' and resid 1202 through 1215 removed outlier: 3.632A pdb=" N LEU B1206 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B1210 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B1214 " --> pdb=" O ASN B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1235 removed outlier: 3.599A pdb=" N GLN B1233 " --> pdb=" O GLY B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1266 removed outlier: 3.539A pdb=" N ASN B1260 " --> pdb=" O ILE B1256 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1297 removed outlier: 3.645A pdb=" N ASN B1291 " --> pdb=" O PRO B1287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B1292 " --> pdb=" O ASN B1288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1296 " --> pdb=" O ALA B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.776A pdb=" N ASP B1316 " --> pdb=" O ASP B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1337 removed outlier: 3.985A pdb=" N ASP B1336 " --> pdb=" O PRO B1332 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1352 removed outlier: 3.540A pdb=" N GLU B1349 " --> pdb=" O SER B1345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1380 removed outlier: 4.203A pdb=" N SER B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1410 removed outlier: 3.702A pdb=" N TYR B1405 " --> pdb=" O ARG B1401 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B1409 " --> pdb=" O TYR B1405 " (cutoff:3.500A) Processing helix chain 'B' and resid 1426 through 1431 removed outlier: 3.530A pdb=" N SER B1431 " --> pdb=" O GLU B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1449 removed outlier: 3.734A pdb=" N ALA B1447 " --> pdb=" O THR B1443 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1478 removed outlier: 3.879A pdb=" N ILE B1474 " --> pdb=" O VAL B1470 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B1476 " --> pdb=" O LYS B1472 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1478 " --> pdb=" O ILE B1474 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1510 removed outlier: 3.545A pdb=" N LYS B1506 " --> pdb=" O THR B1502 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B1507 " --> pdb=" O PRO B1503 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B1510 " --> pdb=" O LYS B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1519 through 1535 removed outlier: 3.686A pdb=" N ASN B1525 " --> pdb=" O GLU B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1548 removed outlier: 3.865A pdb=" N ARG B1546 " --> pdb=" O GLU B1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 874 Processing sheet with id=AA2, first strand: chain 'A' and resid 894 through 897 removed outlier: 6.976A pdb=" N LYS A 894 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER A 944 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 896 " --> pdb=" O SER A 944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1229 through 1232 removed outlier: 6.793A pdb=" N VAL A1202 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE A1232 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A1204 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A1169 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A1203 " --> pdb=" O VAL A1169 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY A1171 " --> pdb=" O ARG A1203 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A1205 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR A1173 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A1080 " --> pdb=" O ILE A1111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A1113 " --> pdb=" O VAL A1080 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A1082 " --> pdb=" O THR A1113 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA A1054 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A1081 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A1056 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG A1083 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A1058 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A1055 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1311 through 1316 removed outlier: 3.678A pdb=" N GLY A1287 " --> pdb=" O PHE A1315 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A1282 " --> pdb=" O GLY A1334 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A1336 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP A1284 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A1338 " --> pdb=" O TRP A1284 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A1286 " --> pdb=" O ILE A1338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 6.603A pdb=" N LYS A1352 " --> pdb=" O GLY A1375 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A1372 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1447 through 1449 removed outlier: 6.356A pdb=" N ILE A1424 " --> pdb=" O GLU A1448 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY A1400 " --> pdb=" O TYR A1425 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A1427 " --> pdb=" O GLY A1400 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A1402 " --> pdb=" O VAL A1427 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASN A1399 " --> pdb=" O VAL A1462 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A1401 " --> pdb=" O LEU A1464 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER A1463 " --> pdb=" O THR A1500 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU A1502 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA A1465 " --> pdb=" O LEU A1502 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 861 through 864 removed outlier: 6.438A pdb=" N ILE B 862 " --> pdb=" O LEU B 961 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 963 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE B 864 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 885 through 886 removed outlier: 6.909A pdb=" N LYS B 885 " --> pdb=" O VAL B 933 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 1220 through 1225 removed outlier: 6.222A pdb=" N VAL B1160 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG B1194 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY B1162 " --> pdb=" O ARG B1194 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B1196 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B1164 " --> pdb=" O VAL B1196 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LYS B1198 " --> pdb=" O TYR B1164 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1137 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B1163 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B1139 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLN B1165 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1071 " --> pdb=" O ILE B1102 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR B1104 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B1073 " --> pdb=" O THR B1104 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B1045 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLU B1072 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B1047 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B1074 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B1049 " --> pdb=" O ARG B1074 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1302 through 1307 removed outlier: 3.729A pdb=" N GLY B1278 " --> pdb=" O PHE B1306 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS B1273 " --> pdb=" O PHE B1324 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B1326 " --> pdb=" O LYS B1273 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY B1325 " --> pdb=" O PRO B1359 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B1363 " --> pdb=" O ILE B1360 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B1343 " --> pdb=" O GLY B1366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1438 through 1440 removed outlier: 6.089A pdb=" N ILE B1415 " --> pdb=" O GLU B1439 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B1416 " --> pdb=" O GLY B1391 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN B1390 " --> pdb=" O VAL B1453 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1455 " --> pdb=" O ASN B1390 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3251 1.34 - 1.46: 1880 1.46 - 1.57: 5058 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10233 Sorted by residual: bond pdb=" C ILE B1329 " pdb=" N THR B1330 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.30e-02 5.92e+03 5.27e+00 bond pdb=" N ARG A1002 " pdb=" CA ARG A1002 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.33e-02 5.65e+03 4.62e+00 bond pdb=" CB VAL B1524 " pdb=" CG2 VAL B1524 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.96e+00 bond pdb=" CG1 ILE A1102 " pdb=" CD1 ILE A1102 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 bond pdb=" CB LEU A1217 " pdb=" CG LEU A1217 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 10228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 13315 2.03 - 4.06: 452 4.06 - 6.10: 60 6.10 - 8.13: 15 8.13 - 10.16: 5 Bond angle restraints: 13847 Sorted by residual: angle pdb=" N VAL A1067 " pdb=" CA VAL A1067 " pdb=" C VAL A1067 " ideal model delta sigma weight residual 113.53 109.04 4.49 9.80e-01 1.04e+00 2.10e+01 angle pdb=" C PHE A1497 " pdb=" N LYS A1498 " pdb=" CA LYS A1498 " ideal model delta sigma weight residual 120.94 129.12 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C GLU A1260 " pdb=" N GLU A1261 " pdb=" CA GLU A1261 " ideal model delta sigma weight residual 122.82 128.48 -5.66 1.42e+00 4.96e-01 1.59e+01 angle pdb=" C VAL A1047 " pdb=" N VAL A1048 " pdb=" CA VAL A1048 " ideal model delta sigma weight residual 122.13 128.28 -6.15 1.85e+00 2.92e-01 1.10e+01 angle pdb=" N GLY A1068 " pdb=" CA GLY A1068 " pdb=" C GLY A1068 " ideal model delta sigma weight residual 115.66 110.55 5.11 1.56e+00 4.11e-01 1.07e+01 ... (remaining 13842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 5367 17.07 - 34.13: 609 34.13 - 51.20: 120 51.20 - 68.26: 27 68.26 - 85.33: 11 Dihedral angle restraints: 6134 sinusoidal: 2450 harmonic: 3684 Sorted by residual: dihedral pdb=" CA MET B1331 " pdb=" C MET B1331 " pdb=" N PRO B1332 " pdb=" CA PRO B1332 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL A1047 " pdb=" C VAL A1047 " pdb=" N VAL A1048 " pdb=" CA VAL A1048 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N PRO A1049 " pdb=" CA PRO A1049 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 964 0.048 - 0.096: 481 0.096 - 0.144: 92 0.144 - 0.192: 20 0.192 - 0.240: 6 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CB VAL B1137 " pdb=" CA VAL B1137 " pdb=" CG1 VAL B1137 " pdb=" CG2 VAL B1137 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL A1381 " pdb=" CA VAL A1381 " pdb=" CG1 VAL A1381 " pdb=" CG2 VAL A1381 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA SER B1279 " pdb=" N SER B1279 " pdb=" C SER B1279 " pdb=" CB SER B1279 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1560 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B1331 " 0.062 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO B1332 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B1332 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B1332 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1502 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B1503 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B1503 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1503 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B1218 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO B1219 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B1219 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1219 " -0.036 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2936 2.80 - 3.33: 8603 3.33 - 3.85: 16690 3.85 - 4.38: 20307 4.38 - 4.90: 33899 Nonbonded interactions: 82435 Sorted by model distance: nonbonded pdb=" OE2 GLU A1081 " pdb=" OG1 THR A1113 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 869 " pdb=" O SER A 938 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR B1050 " pdb=" O PRO B1248 " model vdw 2.296 3.040 nonbonded pdb=" O GLY B 938 " pdb=" OH TYR B 998 " model vdw 2.310 3.040 nonbonded pdb=" O ILE A1037 " pdb=" OG1 THR A1041 " model vdw 2.324 3.040 ... (remaining 82430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 866 through 874 or resid 882 through 1559)) selection = (chain 'B' and (resid 857 through 889 or resid 914 through 964 or resid 992 thro \ ugh 1550)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.110 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 10233 Z= 0.485 Angle : 0.883 10.161 13847 Z= 0.475 Chirality : 0.056 0.240 1563 Planarity : 0.007 0.095 1780 Dihedral : 15.343 85.329 3768 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.17), residues: 1267 helix: -4.79 (0.07), residues: 529 sheet: -2.74 (0.28), residues: 269 loop : -2.70 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1371 HIS 0.005 0.001 HIS B 962 PHE 0.020 0.002 PHE A1026 TYR 0.015 0.002 TYR A1173 ARG 0.017 0.001 ARG A1555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 ARG cc_start: 0.5913 (mtm180) cc_final: 0.5273 (mtm180) REVERT: A 1278 PHE cc_start: 0.8512 (m-10) cc_final: 0.8247 (m-10) REVERT: A 1318 THR cc_start: 0.8473 (m) cc_final: 0.8272 (p) REVERT: A 1324 TYR cc_start: 0.8090 (t80) cc_final: 0.7807 (t80) REVERT: A 1329 ASN cc_start: 0.7590 (t0) cc_final: 0.7349 (p0) REVERT: A 1498 LYS cc_start: 0.7837 (tttm) cc_final: 0.7134 (mmtm) REVERT: A 1537 ASP cc_start: 0.8213 (t0) cc_final: 0.7880 (t0) REVERT: B 1182 TYR cc_start: 0.8426 (t80) cc_final: 0.8161 (t80) REVERT: B 1213 LYS cc_start: 0.8242 (mttp) cc_final: 0.7771 (mtpt) REVERT: B 1302 GLN cc_start: 0.8018 (mt0) cc_final: 0.7722 (mt0) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2761 time to fit residues: 81.2202 Evaluate side-chains 123 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 0.0060 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 HIS A1198 ASN A1209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10233 Z= 0.177 Angle : 0.570 7.707 13847 Z= 0.299 Chirality : 0.043 0.214 1563 Planarity : 0.005 0.090 1780 Dihedral : 5.187 21.842 1366 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.74 % Allowed : 12.19 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.19), residues: 1267 helix: -3.32 (0.15), residues: 529 sheet: -2.18 (0.32), residues: 231 loop : -2.11 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 991 HIS 0.013 0.001 HIS A1417 PHE 0.016 0.001 PHE B1017 TYR 0.018 0.002 TYR A1303 ARG 0.005 0.001 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 PHE cc_start: 0.8500 (m-10) cc_final: 0.8197 (m-10) REVERT: A 1294 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7524 (mmm-85) REVERT: A 1304 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8504 (ttpp) REVERT: A 1329 ASN cc_start: 0.7717 (t0) cc_final: 0.7384 (p0) REVERT: A 1419 MET cc_start: 0.7466 (mtp) cc_final: 0.7166 (mtp) REVERT: A 1537 ASP cc_start: 0.8127 (t0) cc_final: 0.7911 (t0) REVERT: B 965 ARG cc_start: 0.7331 (ttt180) cc_final: 0.5701 (mmm160) REVERT: B 1103 TYR cc_start: 0.8675 (t80) cc_final: 0.8347 (t80) REVERT: B 1213 LYS cc_start: 0.8179 (mttp) cc_final: 0.7743 (mtpt) REVERT: B 1302 GLN cc_start: 0.7931 (mt0) cc_final: 0.7588 (mt0) outliers start: 19 outliers final: 10 residues processed: 154 average time/residue: 0.2372 time to fit residues: 51.2324 Evaluate side-chains 126 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1000 GLU Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1346 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 114 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1189 ASN B1511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10233 Z= 0.148 Angle : 0.516 7.500 13847 Z= 0.264 Chirality : 0.042 0.194 1563 Planarity : 0.004 0.090 1780 Dihedral : 4.693 21.914 1366 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.83 % Allowed : 13.75 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1267 helix: -2.04 (0.19), residues: 526 sheet: -1.82 (0.34), residues: 222 loop : -1.65 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 991 HIS 0.009 0.001 HIS A1417 PHE 0.010 0.001 PHE B1017 TYR 0.014 0.001 TYR A1324 ARG 0.005 0.000 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 PHE cc_start: 0.8436 (m-10) cc_final: 0.8158 (m-10) REVERT: A 1304 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8435 (ttpp) REVERT: A 1446 ASN cc_start: 0.6348 (m-40) cc_final: 0.5890 (p0) REVERT: B 965 ARG cc_start: 0.7227 (ttt180) cc_final: 0.5550 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8165 (t80) cc_final: 0.7857 (t80) REVERT: B 1213 LYS cc_start: 0.8104 (mttp) cc_final: 0.7637 (mtpt) REVERT: B 1302 GLN cc_start: 0.7940 (mt0) cc_final: 0.7628 (mt0) REVERT: B 1414 LYS cc_start: 0.7619 (tppt) cc_final: 0.7022 (ttmt) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 0.2239 time to fit residues: 45.2075 Evaluate side-chains 122 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain B residue 1000 GLU Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 12 optimal weight: 0.0670 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10233 Z= 0.140 Angle : 0.500 7.383 13847 Z= 0.254 Chirality : 0.042 0.190 1563 Planarity : 0.004 0.090 1780 Dihedral : 4.471 19.993 1366 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.47 % Allowed : 15.12 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.23), residues: 1267 helix: -1.37 (0.21), residues: 534 sheet: -1.56 (0.35), residues: 212 loop : -1.45 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 991 HIS 0.007 0.001 HIS A1417 PHE 0.014 0.001 PHE A 890 TYR 0.014 0.001 TYR A 941 ARG 0.003 0.000 ARG A1115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 ARG cc_start: 0.6006 (mtm180) cc_final: 0.5367 (mtm180) REVERT: A 1278 PHE cc_start: 0.8424 (m-10) cc_final: 0.8210 (m-10) REVERT: A 1304 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8503 (ttpp) REVERT: A 1364 ASN cc_start: 0.8243 (p0) cc_final: 0.7949 (p0) REVERT: A 1480 LEU cc_start: 0.7870 (tp) cc_final: 0.7565 (tp) REVERT: B 965 ARG cc_start: 0.7179 (ttt180) cc_final: 0.5485 (mpt-90) REVERT: B 1145 ASN cc_start: 0.7474 (p0) cc_final: 0.7054 (p0) REVERT: B 1182 TYR cc_start: 0.8185 (t80) cc_final: 0.7876 (t80) REVERT: B 1213 LYS cc_start: 0.8064 (mttp) cc_final: 0.7589 (mtpt) REVERT: B 1302 GLN cc_start: 0.7886 (mt0) cc_final: 0.7547 (mt0) REVERT: B 1548 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8623 (t) outliers start: 16 outliers final: 13 residues processed: 127 average time/residue: 0.2208 time to fit residues: 40.0874 Evaluate side-chains 118 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 1000 GLU Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1516 VAL Chi-restraints excluded: chain B residue 1548 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 HIS A 973 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10233 Z= 0.205 Angle : 0.523 7.444 13847 Z= 0.266 Chirality : 0.043 0.199 1563 Planarity : 0.004 0.091 1780 Dihedral : 4.512 21.735 1366 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.29 % Allowed : 14.57 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1267 helix: -0.96 (0.21), residues: 536 sheet: -1.66 (0.33), residues: 234 loop : -1.21 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 991 HIS 0.004 0.001 HIS A1417 PHE 0.009 0.001 PHE A 890 TYR 0.018 0.002 TYR A1036 ARG 0.005 0.000 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 1325 ASP cc_start: 0.7638 (m-30) cc_final: 0.6711 (p0) REVERT: A 1364 ASN cc_start: 0.8225 (p0) cc_final: 0.7935 (p0) REVERT: A 1480 LEU cc_start: 0.7976 (tp) cc_final: 0.7746 (tp) REVERT: B 965 ARG cc_start: 0.7172 (ttt180) cc_final: 0.5499 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8273 (t80) cc_final: 0.7913 (t80) REVERT: B 1191 ASP cc_start: 0.8019 (m-30) cc_final: 0.7804 (m-30) REVERT: B 1213 LYS cc_start: 0.8074 (mttp) cc_final: 0.7690 (ttpt) REVERT: B 1302 GLN cc_start: 0.7924 (mt0) cc_final: 0.7480 (mt0) REVERT: B 1414 LYS cc_start: 0.7641 (tppt) cc_final: 0.7046 (ttmt) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 0.2391 time to fit residues: 43.2129 Evaluate side-chains 116 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1346 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 GLN A 971 HIS A 973 HIS A1446 ASN B1096 HIS B1290 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10233 Z= 0.379 Angle : 0.616 9.131 13847 Z= 0.313 Chirality : 0.046 0.211 1563 Planarity : 0.005 0.096 1780 Dihedral : 4.918 20.990 1366 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 15.12 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1267 helix: -0.92 (0.21), residues: 532 sheet: -1.68 (0.33), residues: 228 loop : -1.24 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 991 HIS 0.005 0.001 HIS B 964 PHE 0.010 0.002 PHE A1497 TYR 0.021 0.002 TYR A 941 ARG 0.006 0.001 ARG B1476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 870 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 1112 TYR cc_start: 0.8333 (t80) cc_final: 0.7744 (t80) REVERT: A 1364 ASN cc_start: 0.8384 (p0) cc_final: 0.8118 (p0) REVERT: A 1498 LYS cc_start: 0.7513 (tptp) cc_final: 0.7133 (tttm) REVERT: A 1558 VAL cc_start: 0.8165 (m) cc_final: 0.7902 (t) REVERT: B 965 ARG cc_start: 0.7580 (ttt180) cc_final: 0.5950 (mpt-90) REVERT: B 1204 ASP cc_start: 0.8192 (m-30) cc_final: 0.7808 (m-30) REVERT: B 1213 LYS cc_start: 0.8135 (mttp) cc_final: 0.7641 (ttpt) REVERT: B 1302 GLN cc_start: 0.7929 (mt0) cc_final: 0.7533 (mt0) REVERT: B 1414 LYS cc_start: 0.7754 (tppt) cc_final: 0.7100 (ttmt) outliers start: 26 outliers final: 20 residues processed: 124 average time/residue: 0.2154 time to fit residues: 38.3746 Evaluate side-chains 122 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1259 ASP Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1336 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10233 Z= 0.200 Angle : 0.551 10.698 13847 Z= 0.276 Chirality : 0.043 0.245 1563 Planarity : 0.004 0.100 1780 Dihedral : 4.633 21.895 1366 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.65 % Allowed : 15.67 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1267 helix: -0.67 (0.22), residues: 542 sheet: -1.54 (0.34), residues: 229 loop : -1.10 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 991 HIS 0.006 0.001 HIS A 973 PHE 0.008 0.001 PHE A1026 TYR 0.034 0.002 TYR A1036 ARG 0.003 0.000 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1179 GLU cc_start: 0.5552 (pm20) cc_final: 0.5264 (pm20) REVERT: A 1364 ASN cc_start: 0.8280 (p0) cc_final: 0.8044 (p0) REVERT: A 1480 LEU cc_start: 0.8022 (tp) cc_final: 0.7787 (tp) REVERT: A 1498 LYS cc_start: 0.7589 (tptp) cc_final: 0.7325 (tttm) REVERT: B 965 ARG cc_start: 0.7331 (ttt180) cc_final: 0.5540 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8166 (t80) cc_final: 0.7919 (t80) REVERT: B 1189 ASN cc_start: 0.8441 (t0) cc_final: 0.8222 (t0) REVERT: B 1204 ASP cc_start: 0.8139 (m-30) cc_final: 0.7787 (m-30) REVERT: B 1213 LYS cc_start: 0.8079 (mttp) cc_final: 0.7575 (ttpt) REVERT: B 1302 GLN cc_start: 0.7887 (mt0) cc_final: 0.7504 (mt0) REVERT: B 1505 MET cc_start: 0.8641 (mtp) cc_final: 0.8426 (mtt) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.2334 time to fit residues: 38.9093 Evaluate side-chains 120 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1336 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1510 GLU Chi-restraints excluded: chain B residue 1516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10233 Z= 0.180 Angle : 0.534 10.652 13847 Z= 0.267 Chirality : 0.043 0.239 1563 Planarity : 0.004 0.100 1780 Dihedral : 4.437 19.123 1366 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.20 % Allowed : 15.40 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1267 helix: -0.38 (0.22), residues: 537 sheet: -1.43 (0.35), residues: 229 loop : -0.96 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.003 0.001 HIS B 999 PHE 0.008 0.001 PHE B1531 TYR 0.024 0.001 TYR A1036 ARG 0.002 0.000 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7283 (mp) REVERT: A 1026 PHE cc_start: 0.7175 (m-80) cc_final: 0.5714 (t80) REVERT: A 1480 LEU cc_start: 0.8035 (tp) cc_final: 0.7776 (tp) REVERT: B 965 ARG cc_start: 0.7305 (ttt180) cc_final: 0.5541 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8202 (t80) cc_final: 0.7904 (t80) REVERT: B 1189 ASN cc_start: 0.8436 (t0) cc_final: 0.8235 (t0) REVERT: B 1204 ASP cc_start: 0.8116 (m-30) cc_final: 0.7792 (m-30) REVERT: B 1213 LYS cc_start: 0.8067 (mttp) cc_final: 0.7555 (ttpt) REVERT: B 1302 GLN cc_start: 0.7895 (mt0) cc_final: 0.7401 (mt0) REVERT: B 1505 MET cc_start: 0.8319 (mtp) cc_final: 0.8059 (mtm) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.2138 time to fit residues: 38.6942 Evaluate side-chains 117 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1336 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1510 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10233 Z= 0.199 Angle : 0.548 10.497 13847 Z= 0.274 Chirality : 0.043 0.245 1563 Planarity : 0.004 0.101 1780 Dihedral : 4.432 20.739 1366 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.83 % Allowed : 16.04 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1267 helix: -0.33 (0.22), residues: 543 sheet: -1.41 (0.35), residues: 234 loop : -0.99 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 991 HIS 0.003 0.001 HIS B 999 PHE 0.008 0.001 PHE B1531 TYR 0.021 0.001 TYR B 953 ARG 0.003 0.000 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7271 (mp) REVERT: A 1026 PHE cc_start: 0.7207 (m-80) cc_final: 0.5711 (t80) REVERT: A 1179 GLU cc_start: 0.5568 (pm20) cc_final: 0.5224 (pm20) REVERT: A 1480 LEU cc_start: 0.8057 (tp) cc_final: 0.7820 (tp) REVERT: A 1558 VAL cc_start: 0.8014 (m) cc_final: 0.7772 (t) REVERT: B 965 ARG cc_start: 0.7317 (ttt180) cc_final: 0.5523 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8217 (t80) cc_final: 0.7912 (t80) REVERT: B 1189 ASN cc_start: 0.8438 (t0) cc_final: 0.8236 (t0) REVERT: B 1204 ASP cc_start: 0.8117 (m-30) cc_final: 0.7805 (m-30) REVERT: B 1213 LYS cc_start: 0.8074 (mttp) cc_final: 0.7546 (ttpt) REVERT: B 1302 GLN cc_start: 0.7897 (mt0) cc_final: 0.7399 (mt0) REVERT: B 1505 MET cc_start: 0.8183 (mtp) cc_final: 0.7942 (mtm) outliers start: 20 outliers final: 19 residues processed: 115 average time/residue: 0.2115 time to fit residues: 35.5008 Evaluate side-chains 118 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1336 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10233 Z= 0.233 Angle : 0.563 10.624 13847 Z= 0.282 Chirality : 0.044 0.251 1563 Planarity : 0.004 0.101 1780 Dihedral : 4.508 19.138 1366 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 16.32 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1267 helix: -0.33 (0.22), residues: 544 sheet: -1.41 (0.35), residues: 229 loop : -0.96 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.003 0.001 HIS B 999 PHE 0.009 0.001 PHE B1531 TYR 0.023 0.002 TYR B 953 ARG 0.004 0.000 ARG B1500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 870 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7264 (mp) REVERT: A 1026 PHE cc_start: 0.7207 (m-80) cc_final: 0.5708 (t80) REVERT: A 1179 GLU cc_start: 0.5581 (pm20) cc_final: 0.5276 (pm20) REVERT: A 1480 LEU cc_start: 0.8031 (tp) cc_final: 0.7770 (tp) REVERT: A 1558 VAL cc_start: 0.8054 (m) cc_final: 0.7820 (t) REVERT: B 965 ARG cc_start: 0.7342 (ttt180) cc_final: 0.5507 (mpt-90) REVERT: B 1182 TYR cc_start: 0.8207 (t80) cc_final: 0.7939 (t80) REVERT: B 1204 ASP cc_start: 0.8080 (m-30) cc_final: 0.7770 (m-30) REVERT: B 1213 LYS cc_start: 0.8116 (mttp) cc_final: 0.7589 (ttpt) REVERT: B 1302 GLN cc_start: 0.7900 (mt0) cc_final: 0.7497 (mt0) outliers start: 21 outliers final: 19 residues processed: 114 average time/residue: 0.2097 time to fit residues: 34.7410 Evaluate side-chains 118 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 973 HIS Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1510 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1336 ASP Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 HIS A1014 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121893 restraints weight = 14001.355| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.41 r_work: 0.3353 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10233 Z= 0.153 Angle : 0.539 10.245 13847 Z= 0.269 Chirality : 0.043 0.243 1563 Planarity : 0.004 0.103 1780 Dihedral : 4.340 20.377 1366 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.56 % Allowed : 17.05 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1267 helix: -0.12 (0.22), residues: 547 sheet: -1.38 (0.35), residues: 228 loop : -0.89 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.003 0.001 HIS A 971 PHE 0.008 0.001 PHE B1531 TYR 0.023 0.001 TYR A1036 ARG 0.003 0.000 ARG A1031 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.90 seconds wall clock time: 44 minutes 7.50 seconds (2647.50 seconds total)